My merge request [1] has just been merged into Qt.
So far, Qt did not find FreeBSD's certificate bundle from the ca_root_nss port
because it was not in its hardcoded path list.
I believe this has not cause many problems so far, but in KDE SC 4.6 the
certificate management code has received some love, and KDE does not use its
own bundle anymore, relying on Qt for that instead.
Since Qt did not find FreeBSD's certificate bundle, any SSL connection would
always trigger that dialog asking the user whether he would accept a secure
connection with an untrusted certificate.
I have hardcoded the path to ca_root_nss's certificate in the code, but in the
Qt port you probably want to replace /usr/local with some variable
representing the port's base path.
I don't know exactly when this patch will start being shipped with Qt
(probably starting from Qt 4.7.2), so it might be better to start shipping it
separately in ports with 4.6 at least.
[1] http://gitorious.org/qt/qt/merge_requests/896